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Long Y, Xu W, Liu C, Dong M, Liu W, Pei X, Li L, Chen R, Jin W. Genetically modified soybean lines exhibit less transcriptomic variation compared to natural varieties. GM CROPS & FOOD 2023; 14:1-11. [PMID: 37454359 DOI: 10.1080/21645698.2023.2233122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 06/29/2023] [Accepted: 06/29/2023] [Indexed: 07/18/2023]
Abstract
Genetically modified (GM) soybeans provide a huge amount of food for human consumption and animal feed. However, the possibility of unexpected effects of transgenesis has increased food safety concerns. High-throughput sequencing profiling provides a potential approach to directly evaluate unintended effects caused by foreign genes. In this study, we performed transcriptomic analyses to evaluate differentially expressed genes (DEGs) in individual soybean tissues, including cotyledon (C), germ (G), hypocotyl (H), and radicle (R), instead of using the whole seed, from four GM and three non-GM soybean lines. A total of 3,351 DEGs were identified among the three non-GM soybean lines. When the GM lines were compared with their non-GM parents, 1,836 to 4,551 DEGs were identified. Furthermore, Gene Ontology (GO) analysis of the DEGs showed more abundant categories of GO items (199) among non-GM lines than between GM lines and the non-GM natural varieties (166). Results of Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that most KEGG pathways were the same for the two types of comparisons. The study successfully employed RNA sequencing to assess the differences in gene expression among four tissues of seven soybean varieties, and the results suggest that transgenes do not induce massive transcriptomic alterations in transgenic soybeans compared with those that exist among natural varieties. This work offers empirical evidence to investigate the genomic-level disparities induced by genetic modification in soybeans, specifically focusing on seed tissues.
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Affiliation(s)
- Yan Long
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wentao Xu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China
| | - Caiyue Liu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Mei Dong
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Weixiao Liu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xinwu Pei
- Biotechnology Research Institute, Tianjin Academy of Agricultural Sciences, Tianjin, China
| | - Liang Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Rui Chen
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wujun Jin
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
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Elevated CO 2 alters transgene methylation not only in promoterregion but also in codingregion of Bt rice under different N-fertilizer levels. Sci Rep 2020; 10:18138. [PMID: 33097753 PMCID: PMC7584594 DOI: 10.1038/s41598-020-75121-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 10/09/2020] [Indexed: 11/08/2022] Open
Abstract
The earth has been undergoing climate change, especially in recent years, driven by increasing concentration of atmospheric carbon dioxide (CO2) and rising earth-surface temperature, which could reduce N allocation to Bt toxin for transgenic Bt crops (Bt crops), but the N fertilization is considered to be an effective method to enhance the C-N balance in Bt crops in the case of elevated CO2 in future. DNA methylation not only in promoterregion but also in codingregion of transgene plays a critical role in transgene expression regulation and silencing of transgenic crops. Recent research has emphasized the risks of increased transgene silencing of Bacillus thuringiensis (Bt) rice under elevated CO2. In this study, the effects of elevated CO2 (vs. ambient CO2) on exogenous Bt toxins and transgene expression in promoterregion and codingregion of Bt rice during tillering stage (cv. HH1 expressing fused Cry1Ab/Cry1Ac) were evaluated under three nitrogen (N) fertilizer rate (1/4, 1 and 2 N levels). The aboveground and belowground biomass, and foliar Bt protein content of Bt rice were all significantly increased with the augmentation of N-fertilizer. And elevated CO2 significantly increased belowground biomass, total soluble protein content, transgene methylation levels in promoterregion (P1), and in total of promoterregion(P1) and codingregion (P2 + P3) (i.e., P1 + P2 + P3) at 1 N level, and it also increased transgene methylation levels in codingregion (P2), and in total of promoterregion and codingregion (P1 + P2 + P3) at 2 N level. In addition, elevated CO2 decreased foliar Bt protein content at 1 N level. The transgene methylation levels in promoterregion and codingregion were negatively correlated with Bt-transgene expression level. The methylation level of cytosines located at CG sites was higher than those at CHG and CHH sites in P1, P2 and P3 fragments regardless of the CO2 or N-fertilizer level. The correlation of transgene mehtylation in promoterregion with transgene expression is even stronger than that in codingregion. These data indicate that N fertilization supply will increase the Bt toxin content in transgenic Bt rice, especially under elevated CO2.
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Yu J, Xu F, Wei Z, Zhang X, Chen T, Pu L. Epigenomic landscape and epigenetic regulation in maize. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1467-1489. [PMID: 31965233 DOI: 10.1007/s00122-020-03549-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Accepted: 01/14/2020] [Indexed: 05/12/2023]
Abstract
Epigenetic regulation has been implicated in the control of multiple agronomic traits in maize. Here, we review current advances in our understanding of epigenetic regulation, which has great potential for improving agronomic traits and the environmental adaptability of crops. Epigenetic regulation plays vital role in the control of complex agronomic traits. Epigenetic variation could contribute to phenotypic diversity and can be used to improve the quality and productivity of crops. Maize (Zea mays L.), one of the most widely cultivated crops for human food, animal feed, and ethanol biofuel, is a model plant for genetic studies. Recent advances in high-throughput sequencing technology have made possible the study of epigenetic regulation in maize on a genome-wide scale. In this review, we discuss recent epigenetic studies in maize many achieved by Chinese research groups. These studies have explored the roles of DNA methylation, posttranslational modifications of histones, chromatin remodeling, and noncoding RNAs in the regulation of gene expression in plant development and environment response. We also provide our future prospects for manipulating epigenetic regulation to improve crops.
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Affiliation(s)
- Jia Yu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Fan Xu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ziwei Wei
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Xiangxiang Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Tao Chen
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Li Pu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China.
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Fan X, Chen J, Wu Y, Teo C, Xu G, Fan X. Genetic and Global Epigenetic Modification, Which Determines the Phenotype of Transgenic Rice? Int J Mol Sci 2020; 21:E1819. [PMID: 32155767 PMCID: PMC7084647 DOI: 10.3390/ijms21051819] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Revised: 02/28/2020] [Accepted: 03/01/2020] [Indexed: 01/17/2023] Open
Abstract
Transgenic technologies have been applied to a wide range of biological research. However, information on the potential epigenetic effects of transgenic technology is still lacking. Here, we show that the transgenic process can simultaneously induce both genetic and epigenetic changes in rice. We analyzed genetic, epigenetic, and phenotypic changes in plants subjected to tissue culture regeneration, using transgenic lines expressing the same coding sequence from two different promoters in transgenic lines of two rice cultivars: Wuyunjing7 (WYJ7) and Nipponbare (NP). We determined the expression of OsNAR2.1 in two overexpression lines generated from the two cultivars, and in the RNA interference (RNAi) OsNAR2.1 line in NP. DNA methylation analyses were performed on wild-type cultivars (WYJ7 and NP), regenerated lines (CK, T0 plants), segregation-derived wild-type from pOsNAR2.1-OsNAR2.1 (SDWT), pOsNAR2.1-OsNAR2.1, pUbi-OsNAR2.1, and RNAi lines. Interestingly, we observed global methylation decreased in the T0 regenerated line of WYJ7 (CK-WJY7) and pOsNAR2.1-OsNAR2.1 lines but increased in pUbi-OsNAR2.1 and RNAi lines of NP. Furthermore, the methylation pattern in SDWT returned to the WYJ7 level after four generations. Phenotypic changes were detected in all the generated lines except for SDWT. Global methylation was found to decrease by 13% in pOsNAR2.1-OsNAR2.1 with an increase in plant height of 4.69% compared with WYJ7, and increased by 18% in pUbi-OsNAR2.1 with an increase of 17.36% in plant height compared with NP. This suggests an absence of a necessary link between global methylation and the phenotype of transgenic plants with OsNAR2.1 gene over-expression. However, epigenetic changes can influence phenotype during tissue culture, as seen in the massive methylation in CK-WYJ7, T0 regenerated lines, resulting in decreased plant height compared with the wild-type, in the absence of a transformed gene. We conclude that in the transgenic lines the phenotype is mainly determined by the nature and function of the transgene after four generations of transformation, while the global epigenetic modification is dependent on the genetic background. Our research suggests an innovative insight in explaining the reason behind the occurrence of transgenic plants with random and undesirable phenotypes.
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Affiliation(s)
- Xiaoru Fan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, MOA Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Nanjing Agricultural University, Nanjing 210095, China; (X.F.); (J.C.); (G.X.)
| | - Jingguang Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, MOA Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Nanjing Agricultural University, Nanjing 210095, China; (X.F.); (J.C.); (G.X.)
- CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute in Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518116, China
| | - Yufeng Wu
- Bioinformatics Center, Nanjing Agricultural University, Nanjing 210095, China;
| | - CheeHow Teo
- Centre of Research in Biotechnology for Agriculture (CEBAR), University of Malaya, 50603 Kuala Lumpur, Malaysia;
| | - Guohua Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, MOA Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Nanjing Agricultural University, Nanjing 210095, China; (X.F.); (J.C.); (G.X.)
| | - Xiaorong Fan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, MOA Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Nanjing Agricultural University, Nanjing 210095, China; (X.F.); (J.C.); (G.X.)
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Zhao Q, Du Y, Wang H, Rogers HJ, Yu C, Liu W, Zhao M, Xie F. 5-Azacytidine promotes shoot regeneration during Agrobacterium-mediated soybean transformation. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2019; 141:40-50. [PMID: 31128562 DOI: 10.1016/j.plaphy.2019.05.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 04/07/2019] [Accepted: 05/14/2019] [Indexed: 05/27/2023]
Abstract
Agrobacterium-mediated soybean transformation has been greatly improved in recent years, however the transformation efficiency is still low and highly genotype-dependent when compared to other species. Here, we characterized seventeen soybean genotypes based on their genetic transformation efficiencies, i.e., high and low, during Agrobacterium-mediated transformation. To reveal the molecular basis of this transformation difference, we constructed a highly efficient transient transgene expression system using soybean cotyledon protoplasts and then assess the methylation levels of promoter and coding regions of an EYFP (enhanced yellow fluorescent protein) gene introduced into the protoplast cultures of various soybean genotypes using BSP (bisulfite sequencing PCR). Increased methylation was found to be associated with the considerably decreased transfection efficiency (as percentage of EYFP fluorescent protoplasts) in low-efficacy genotypes as compared with those in high-efficacy on three DAT (day after transfection). 5-Azacytidine (5-Azac), a demethylating reagent commonly applied in epigenetic researches, significantly improved the transient transfection efficiency and transgene expression level in low-efficiency genotypes. Furthermore, the shoot regeneration efficiency in low-efficiency genotypes was substantially increased by 5-Azac treatment in an Agrobacterium-mediated soybean transformation system. Taken together, we concluded that lower methylation level in transgene contributed to enhanced shoot regeneration in Agrobacterium-mediated soybean transformation.
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Affiliation(s)
- Qiang Zhao
- Agricultural College, Shenyang Agricultural University, Shenyang, 10866, PR China.
| | - Yanli Du
- Agricultural College, Shenyang Agricultural University, Shenyang, 10866, PR China.
| | - Hetong Wang
- College of Life Science and Bioengineering, Shenyang University, Shenyang, 110044, PR China.
| | - Hilary J Rogers
- Cardiff University, School of Biosciences, Cardiff, CF10 3TL, UK.
| | - Cuimei Yu
- Agricultural College, Shenyang Agricultural University, Shenyang, 10866, PR China.
| | - Wan Liu
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110016, PR China.
| | - Mingzhe Zhao
- Agricultural College, Shenyang Agricultural University, Shenyang, 10866, PR China.
| | - Futi Xie
- Agricultural College, Shenyang Agricultural University, Shenyang, 10866, PR China.
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Abreu FRM, Dedicova B, Vianello RP, Lanna AC, de Oliveira JAV, Vieira AF, Morais OP, Mendonça JA, Brondani C. Overexpression of a phospholipase (OsPLDα1) for drought tolerance in upland rice (Oryza sativa L.). PROTOPLASMA 2018; 255:1751-1761. [PMID: 29846801 DOI: 10.1007/s00709-018-1265-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 05/15/2018] [Indexed: 06/08/2023]
Abstract
This work aimed to evaluate the drought tolerance of transformed plants of the cultivar BRSMG Curinga that overexpress the rice phospholipase D α1 (OsPLDα1) gene. The productivity of independent transformation event plants of the OsPLDα1 gene was evaluated in an experiment where 19 days of water deficit were applied at the reproductive stage, a very strict growing condition for upland rice. The non-genetically modified cultivar (NGM) under drought treatment reduced productivity by 89% compared with that under irrigated treatment, whereas transformed plants (PLDα1_E2) reduced productivity by only 41%. After the drought treatment, the PLDα1_E2 plants productivity was five times greater than that of the NGM plant. Moreover, no adverse effects on growth and development of the transgenic plants were observed. Seven days after the resumption of irrigation, PLDα1_E2 plants had higher stomatal conductance, greater photosynthetic rate, and transpiration rate than did NGM plants, as well as a higher expression level of the OsPLDα1 gene. A delay in the senescence process was observed in these PLDα1_E2 plants, and this was determined for the recovery of photosynthesis, with greater expression of the Rubisco and lower expression of the SOD. This finding was suggestive of decreased oxidative stress, probably due to gas exchange by the partial closure of the stomata of these transformed plants, which prevented the formation of reactive oxygen species. OsPLDα1 gene overexpression resulted in a reduction in production loss under severe water deficit and revealed a possibility for the development of upland rice cultivars that are more tolerant to extreme drought conditions.
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Affiliation(s)
| | - Beata Dedicova
- International Center for Tropical Agriculture A.A. 6713, Cali, Colombia
| | | | - Anna Cristina Lanna
- Embrapa Arroz e Feijão, Rodovia GO-462, Km 12, Santo Antônio de Goiás, Goiás, Brazil
| | | | - Ariadna Faria Vieira
- Escola de Agronomia, Universidade Federal de Goiás, Santo Antônio de Goiás, Goiás, Brazil
| | - Odilon Peixoto Morais
- Embrapa Arroz e Feijão, Rodovia GO-462, Km 12, Santo Antônio de Goiás, Goiás, Brazil
| | - João Antônio Mendonça
- Embrapa Arroz e Feijão, Rodovia GO-462, Km 12, Santo Antônio de Goiás, Goiás, Brazil
| | - Claudio Brondani
- Embrapa Arroz e Feijão, Rodovia GO-462, Km 12, Santo Antônio de Goiás, Goiás, Brazil.
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Ben Ali SE, Schamann A, Dobrovolny S, Indra A, Agapito-Tenfen SZ, Hochegger R, Haslberger AG, Brandes C. Genetic and epigenetic characterization of the cry1Ab coding region and its 3′ flanking genomic region in MON810 maize using next-generation sequencing. Eur Food Res Technol 2018. [DOI: 10.1007/s00217-018-3062-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Kumari J, Udawat P, Dubey AK, Haque MI, Rathore MS, Jha B. Overexpression of SbSI-1, A Nuclear Protein from Salicornia brachiata Confers Drought and Salt Stress Tolerance and Maintains Photosynthetic Efficiency in Transgenic Tobacco. FRONTIERS IN PLANT SCIENCE 2017; 8:1215. [PMID: 28751902 PMCID: PMC5508026 DOI: 10.3389/fpls.2017.01215] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 06/27/2017] [Indexed: 05/14/2023]
Abstract
A novel Salicornia brachiata Salt Inducible (SbSI-1) gene was isolated and overexpressed in tobacco for in planta functional validation subjected to drought and salt stress. SbSI-1 is a nuclear protein. The transgenic tobacco overexpressing SbSI-1 gene exhibited better seed germination, growth performances, pigment contents, cell viability, starch accumulation, and tolerance index under drought and salt stress. Overexpression of SbSI-1 gene alleviated the build-up of reactive oxygen species (ROS) and curtailed the ROS-induced oxidative damages thus improved the physiological health of transgenic tobacco under stressed conditions. The higher activities of antioxidant enzymes, lower accumulation of ROS, higher membrane stability, relative water content, and polyphenol contents indicated the better survival of the transgenic tobacco than wild-type (WT) tobacco under stressed conditions. Transgenic tobacco had a higher net photosynthetic rate, PSII operating efficiency, and performance index under drought and salt stress. Higher accumulation of compatible solutes and K+/Na+ ratio in transgenic tobacco than WT showed the better osmotic and redox homeostasis under stressed conditions. The up-regulation of genes encoding antioxidant enzymes (NtSOD, NtAPX, and NtCAT) and transcription factors (NtDREB2 and NtAP2) in transgenic tobacco under stressed conditions showed the role of SbSI-1 in ROS alleviation and involvement of this gene in abiotic stress tolerance. Multivariate data analysis exhibited statistical distinction among growth responses, physiological health, osmotic adjustment, and photosynthetic responses of WT and transgenic tobacco under stressed conditions. The overexpression of SbSI-1 gene curtailed the ROS-induced oxidative damages and maintained the osmotic homeostasis under stress conditions thus improved physiological health and photosynthetic efficiencies of the transgenic tobacco overexpressing SbSI-1 gene.
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Affiliation(s)
- Jyoti Kumari
- Marine Biotechnology and Ecology Division, CSIR-Central Salt and Marine Chemicals Research Institute, Council of Scientific and Industrial ResearchBhavnagar, India
- Academy of Scientific and Innovative Research, Council of Scientific and Industrial ResearchNew Delhi, India
| | - Pushpika Udawat
- Marine Biotechnology and Ecology Division, CSIR-Central Salt and Marine Chemicals Research Institute, Council of Scientific and Industrial ResearchBhavnagar, India
- Academy of Scientific and Innovative Research, Council of Scientific and Industrial ResearchNew Delhi, India
| | - Ashish K. Dubey
- Marine Biotechnology and Ecology Division, CSIR-Central Salt and Marine Chemicals Research Institute, Council of Scientific and Industrial ResearchBhavnagar, India
| | - Md Intesaful Haque
- Marine Biotechnology and Ecology Division, CSIR-Central Salt and Marine Chemicals Research Institute, Council of Scientific and Industrial ResearchBhavnagar, India
| | - Mangal S. Rathore
- Marine Biotechnology and Ecology Division, CSIR-Central Salt and Marine Chemicals Research Institute, Council of Scientific and Industrial ResearchBhavnagar, India
- Academy of Scientific and Innovative Research, Council of Scientific and Industrial ResearchNew Delhi, India
- *Correspondence: Mangal S. Rathore ;
| | - Bhavanath Jha
- Marine Biotechnology and Ecology Division, CSIR-Central Salt and Marine Chemicals Research Institute, Council of Scientific and Industrial ResearchBhavnagar, India
- Academy of Scientific and Innovative Research, Council of Scientific and Industrial ResearchNew Delhi, India
- Bhavanath Jha
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